This is an amended version of a grant to further develop two-hybrid technology and to integrate two hybrid data with other information necessary for its interpretation. The PI proposes three specific aims during the next five years (from the proposal): 1) Continue development of the protein interaction database (Interaction). They will continue to enter data from their own experiments and other public sources. They will develop a satellite database for data input by others without curation on their part. They will disseminate the database and the computational tools, including search programs, data input/output tools, and programs to conjoin interaction data with other genomic data, as these are developed. 2) Continue to amass potential interacting proteins and test their interactions. To gain a measure of the ability to predict protein interactions, they will focus on interaction among proteins from C. elegans followed by D. melanogaster that contain identifiable conserved supersecondary structures. They will construct new bait and prey plasmids that display representative substructure, add them to their existing collection, and test the entire collection for interactions by interaction mating. They will work with a number of structural biology laboratories to identify additional subdomains from proteins encoded by these organisms and test their interactions. 3) Develop computational methods to use interactions in concert with other data types. They will first devise methods to join interaction data with sequence data, then with gene expression data obtained from microarrays beta-test these tools by applying them in the context of a translational biomedical research center.